A5004058551- Plant Pathogens and Fungal Diseases
- Species Distribution and Climate Change
- Music and Audio Processing
- Animal Vocal Communication and Behavior
- Mycorrhizal Fungi and Plant Interactions
- Neural Networks and Applications
- Plant-Microbe Interactions and Immunity
- Speech and Audio Processing
- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Plant Disease Resistance and Genetics
- Plant Pathogens and Resistance
- Speech Recognition and Synthesis
- Microbial Inactivation Methods
- Plant Pathogenic Bacteria Studies
- Plant and animal studies
- Clostridium difficile and Clostridium perfringens research
- Marine animal studies overview
- Botulinum Toxin and Related Neurological Disorders
- Gene expression and cancer classification
- Identification and Quantification in Food
- Forest Ecology and Biodiversity Studies
- Ecology and Vegetation Dynamics Studies
- Yersinia bacterium, plague, ectoparasites research
- Lichen and fungal ecology
University of Helsinki
2015-2024
Swedish University of Agricultural Sciences
2021
Czech Academy of Sciences, Institute of Biotechnology
2014
Helsinki Institute of Physics
2008-2013
Ministry of Economic Affairs and Employment
2012
Helsinki Institute for Information Technology
2009
Research Institute of the Finnish Economy
2008
University of California, Berkeley
2003
International Computer Science Institute
2003
Nokia (Finland)
1997
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report genome (393 Mb) Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a recognized model species metapopulation biology and eco-evolutionary research, which putative ancestral karyotype n=31. Using phylogenetic analyses Nymphalidae other Lepidoptera, combined with orthologue-level comparisons chromosomes,...
Photoassimilates such as sugars are transported through phloem sieve element cells in plants. Adapted for effective transport, elements develop enucleated living cells. We used electron microscope imaging and three-dimensional reconstruction to follow morphogenesis Arabidopsis. show that differentiation involves enucleation, which the nuclear contents released degraded cytoplasm at same time other organelles rearranged cytosol is degraded. These cellular reorganizations orchestrated by...
This paper is related to the development of signal processing techniques for automatic recognition bird species. Three different parametric representations are compared. The first representation based on sinusoidal modeling which has been earlier found useful highly tonal sounds. Mel-cepstrum parameters used since they have very in parallel problem speech recognition. Finally, a vector various descriptive features tested because such models popular audio classification applications, and song...
When targeted to a barcoding region, high-throughput sequencing can be used identify species or operational taxonomical units from environmental samples, and thus study the diversity structure of communities. Although there are many methods which provide confidence scores for assigning taxonomic affiliations, it is not straightforward translate these values unbiased probabilities. We present probabilistic method classification (PROTAX) DNA sequences. Given pre-defined tree that partially...
Summary A crucial step in the use of DNA markers for biodiversity surveys is assignment Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows all information known based on taxonomic names. Taxonomic placement barcoding sequences inherently probabilistic because contain errors, there natural variation among within a species, and reference data bases are incomplete can have false annotations. However, most existing bioinformatics methods either exclude uncertainty, or...
The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate captured 62% total haplotype diversity show most species possess a few common haplotypes many rare ones. Specimens in dataset have an average 95.3%...
Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates placement fungal sequences. We developed Protax-fungi, a general tool for internal transcribed spacer (ITS) sequences, implemented it into the PlutoF platform UNITE database molecular identification fungi. With empirical data on root- wood-associated fungi, Protax-fungi reliably identified (with at least 90% probability) majority sequences to order level but only around one-fifth them species...
Abstract Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes are relevant well-being. Fungi megadiverse kingdom plays key role and affects How urbanization influences fungi has remained poorly understood, partially due to methodological difficulties comprehensively surveying fungi. Here we show both aerial soil fungal communities greatly poorer urban than natural areas. Strikingly, fivefold reduction DNA abundance...
Abstract Fungi are among the most diverse and ecologically important kingdoms in life. However, distributional ranges of fungi remain largely unknown as do ecological mechanisms that shape their distributions 1,2 . To provide an integrated view spatial seasonal dynamics fungi, we implemented a globally distributed standardized aerial sampling fungal spores 3 The vast majority operational taxonomic units were detected within only one climatic zone, spatiotemporal patterns species richness...
Abstract Global biodiversity gradients are generally expected to reflect greater species replacement closer the equator. However, empirical validation of global largely relies on vertebrates, plants, and other less diverse taxa. Here we assess temporal spatial dynamics arthropod using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps deployed monitor changes in communities. Overall, encountered more than 150,000 unique barcode index numbers (BINs) (i.e....
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and important for human health, food production nature conservation. Our knowledge on fungal diversity ecology is however still very limited, part because surveying identifying fungi time demanding requires expert knowledge. We present method that allows anyone to generate list species likely occur region interest, with minimal effort without requiring taxonomical expertise. The consists using cyclone...
Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys on Barro Colorado Island (BCI), Panama, which well-known mammal community, and compared our results against diurnal transect counts camera trapping. We collected 1,084 in 29 sampling days, with mammal-specific (16S) vertebrate-specific (12S) primers, sequenced amplicons Illumina MiSeq. For taxonomic...
Abstract Inbreeding is common in nature, and many laboratory studies have documented that inbreeding depression can reduce the fitness of individuals. Demonstrating consequences on growth persistence populations more challenging because are often regulated by density‐ or frequency‐dependent selection influenced demographic environmental stochasticity. A few empirical shown increase extinction risk local populations. The importance at metapopulation level has been conjectured based...
To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated Linnaean taxonomy. In this study, (1) report the creation of a comprehensive library DNA barcodes for arthropods an entire country (Finland), (2) publish library, and (3) deliver new identification tool insects spiders, as based on resource. The contains mtDNA COI 11,275 (43%) 26,437 arthropod species known from Finland, including 10,811 (45%) 23,956 insect species....
Abstract An automatic bird sound recognition system is a useful tool for collecting data of different species ecological analysis. Together with autonomous recording units (ARUs), such provides possibility to collect observations on scale that no human observer could ever match. During the last decades, progress has been made in field recognition, but recognizing from untargeted soundscape recordings remains challenge. In this article, we demonstrate workflow building global identification...
Novel methods for sampling and characterizing biodiversity hold great promise re-evaluating patterns of life across the planet. The airborne spores with a cyclone sampler, sequencing their DNA, have been suggested as an efficient well-calibrated tool surveying fungal diversity various environments. Here we present data originating from Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations world. Each sample represents DNA extracted 24 m
Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) which causes spoilage in cold-stored modified-atmosphere-packaged (MAP) meat products. In addition to the fermentative metabolism, L. able respire when exogenous heme and oxygen are available. this study, we investigated respiration effects on growth rate, biomass, gene expression, volatile organic compound (VOC) production laboratory media pork loin. The samples were evaluated by sensory panel every second or third...
Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different are labeled by attaching a short sample specific nucleotide sequence, barcode, each DNA molecule prior pooling them into mix containing number of libraries be sequenced simultaneously. After sequencing, the binned identifying barcode within read. In order tolerate errors, barcodes should sufficiently apart from other space. An additional constraint due both usage and basecalling...
The kingdom Fungi is a megadiverse group represented in all ecosystem types. global diversity and distribution of fungal taxa are poorly known, part due to the limitations related traditional fruit-body survey methods. These previous hurdles now being overcome by rapidly developing DNA-based surveys. Past DNA surveys have predominantly examined soil samples, which capture high species but represent only local community. Recent work has shown that samples collected from air with cyclone...
Understanding the role of interspecific interactions in shaping ecological communities is one central goals community ecology. In fungal communities, measuring directly challenging because these are composed large numbers species, many which unculturable. An indirect way assessing determining structure to identify species co-occurrences that not constrained by environmental conditions. this study, we investigated among root-associated fungi, asking whether fungi co-occur more or less...
DOI: 10.1111/j.1469-8137.2009.02931.x Commentary p 237
Pectobacterium atrosepticum is a Gram-negative plant-pathogenic bacterium that rots potato stems and tubers. Microarray analysis was used to identify genes were differentially expressed when host extracts added the growth medium. Potato downregulated expression of ribosomal related uptake metabolism nutrients, upregulated needed for nitrate or phosphonate use. Some observed changes in gene host-extract-induced cultures are similar those during attachment tissues. Other responses indicated...